Biochemical Applications Research Articles

An Sub-Micron Double-Layer Capacitance of a Microwell Array for Biomolecular Sensing

The interface between a solid and a liquid gives rise to the electric double layer (EDL) through the ion redistribution phenomenon. This effectively neutralizes the surface charges of the solid, and the relationship between the EDL and surface potential is crucial. Although surface potential can be a useful indicator of surface properties, measuring it using existing techniques like kelvin probe microscopy and electroosmotic mobility measurement is challenging as they are complex and difficult to implement as in-situ monitoring techniques.To address this demand, we used a vertical metal-oxide-metal microwells array to decrease the distance between electrodes and measure EDL capacitance changes induced by surface modifications. The device was fabricated using a layer-by-layer deposition method followed by photolithography and multiple dry etching steps. The diameter of well is around 3 um as SEM image shows. The distance between two electrodes could be scaled down to 100 nm by this method to achieve outstanding characteristics. Cyclic voltammetry was used to accurately estimate surface potential changes. Based on this method, the slope of charging current vs scan rate will be the EDLC.Next, we demonstrated its potential by detecting Avidin with excellent sensitivity. We applied APTES as the first layer on the sidewall of wells, then NHS-Biotin as the second layer to convert the amine group to an biotin group on the side wall surface. Finally we will immobilize the avidin. The capacitor has significant changed after introducing the avidin onto the sidewall of wells. And the concentration could be low to 100pg/mL for avidin sensing.Our innovative metrological architecture can be used in diverse biochemical applications to characterize surface-interfaces in real-time. Figure 1

ZIF-based boronic acid modified molecular imprinted polymers in combination with silver nanoparticles/glutathione coated graphene oxide adsorbent for the selective enrichment of ellagic acid

This study focuses on the extraction of ellagic acid (EA), a valued phenolic compound, from agricultural waste chestnut shell samples. A novel approach is introduced using a combination of boronic acid-modified molecularly imprinted polymer (ZIF@B@MIP) and a nanocomposite of graphene oxide-coated silver nanoparticles (GO@Ag@GSH) to enhance EA enrichment. ZIF@B@MIP precisely captured EA through boronate affinity-based molecular imprinting recognition. ZIF@B@MIP employs boronate affinity-based molecular imprinting recognition to precisely capture EA, while GO@Ag@GSH provides ample adsorption sites. The synergistic effect of ZIF@B@MIP and GO@Ag@GSH demonstrates excellent enrichment capability and selectivity for EA. High-performance liquid chromatography (HPLC) is employed for sensitive EA detection, achieving a maximum adsorption capacity of 46.25 mg g–1 and an imprinting factor of 3.01. The adsorption capacity to different structural analogue was investigated, and the selectivity coefficient was used to evaluate the selectivity, and its value was 1.16–3.01. The method successfully enriches EA in chestnut shell samples with a recovery rate of 95.6 %–110.1 %. This research presents an innovative approach for effective phenolic components enrichment from natural resources for pharmaceutical and biochemical applications.

Generalized Michaelis-Menten rate law with time-varying molecular concentrations.

The Michaelis-Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry, biophysics, cell biology, systems biology, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than the molecular concentrations change. Yet, this assumption is not always justified. Here, we relax this quasi-steady state requirement and propose the generalized MM rate law for the interactions of molecules with active concentration changes over time. Our approach for time-varying molecular concentrations, termed the effective time-delay scheme (ETS), is based on rigorously estimated time-delay effects in molecular complex formation. With particularly marked improvements in protein-protein and protein-DNA interaction modeling, the ETS provides an analytical framework to interpret and predict rich transient or rhythmic dynamics (such as autogenously-regulated cellular adaptation and circadian protein turnover), which goes beyond the quasi-steady state assumption.

Multi-reflection Astral mass spectrometer with isochronous drift in elongated ion mirrors

Multi-reflection time-of-flight (MR ToF) mass spectrometers are promising tools for accurate mass analysis, which combine a high resolving power with a short duty cycle. Though MR ToFs have been used for long in nuclear physics to explore short-lived isotopes, a restricted mass range of closed ion traps did not allow their use in chemical and bio-chemical applications, in which an analyte mixture contains a wide range of ionic species. This paper describes development of an open-path multi-reflection analyzer in which ion trajectories stay separated in the phase space on the oscillations to achieve an unlimited mass range. The design employs a controlled adiabatic ion drift along electrostatic mirrors. Ion focusing and time-of-flight aberration are corrected via reflection in slightly converging mirrors and refraction on optimally shaped electrostatic prisms.

Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins.

Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.

Gas-phase ion chemistry of [B12X12]2− (X = F, Cl, Br, I, CN). A brief review of twelve years of researching twelve−vertexed dianions and their fragments

The closo-dodecaborate dianions [B12X12]2− (X = halogen, CN) have been recognized in recent years for their outstanding physical and chemical properties. Gas-phase ion chemistry and spectroscopy have contributed to the understanding and further development of their record stability, which is applied to stabilize highly reactive cations. Fragment ions generated by collision induced dissociation provide access to a large variety of boron-based structures previously not available in the condensed phase and have challenged common chemical concepts (e.g., the discovery of “superelectrophilic anions”). This has opened new avenues for noble gas chemistry and direct functionalization of alkyl groups with covalently bound “charge tags”. Furthermore, the interactions with neutral molecules in the gas phase, e.g., host-guest chemistry, complements the fundamental understanding of solvation effects in solution and association with large neutral molecules, which is highly relevant for the biochemical applications of these compounds. Future perspectives, in particular the special role of these ions and their fragments in preparative mass spectrometry, are discussed.

Search of electron-rich and electron-deficient building blocks through data mining and library generation for the designing of polymers for organic solar cells

Typical designing of the organic molecules for numerous chemical, biochemical, and electrochemical applications requires extensive human workforce, conceptual intuition, far-reaching academic literature survey, and laborious experimentation. Recently, data-driven approaches, peculiarly machine learning (ML) analysis, have emerged as an alternative methodology to these traditional designing methods. These ML approaches provide robust and quicker way to address the serious restrictions of unavailability of work space, painstaking experimentation, and reduction in the number of experimental trials. In present study, two reference compounds, 5,6-difluoro-2-methylbenzo [d] thiazole and benzo [1,2-b: 3,4-b': 6,5-b''] trithiophene were selected as standard reference compounds. The ChemSpace database was mined for screening the potential effective building blocks and the new libraries of the organic molecules (having high similarity correlation with the reference compounds) were generated for designing the organic solar cell (OSC) devices. The ML analysis was also performed to predict the reorganization energy. The newly designed molecules were further evaluated with respect to their synthetic viability and electronic distribution characteristics to computationally excess the applicability of these novel organic molecules for the OSCs devices. The work presented in this study provides an alternative methodology for the selection of novel organic molecules for developing high-performance OSCs devices.

Quantitative mixed-valence state identification of metal ions based on fluorescence response of graphene quantum dots

Quantitative identification of mixed-valence metal ions is essential for gaining deeper insights into critical chemical and biological processes in environmental science, chemical engineering, and biological systems. However, a simple approach of quantitative identification mixed-valence metal ions in solution has remained a challenge. In this study, we have experimentally observed a significant linear correlation (R2 = 0.99) between the concentration of high-valence metal ions (using iron ions as an example) and the fluorescence intensity of graphene quantum dots (GQDs). Utilizing the distinct fluorescence responses of GQDs to high-valence and low-valence metal ions, reliable quantitative detection of mixed-valence metal ions has been successfully achieved. Remarkably, we introduced real-time monitoring of mixed-valence metal ions, revealing a shift from a molar ratio of approximately 4.0 to 2.0. Density functional theory calculations have revealed significant differences in charge transfer between high-valence and low-valence states of metal ions adsorbed onto GQDs. Furthermore, the versatility of this method can extend to various types of GQDs and metal ions, highlighting its universal applicability. This work presents a simple, convenient, and cost-effective approach for quantitatively identifying mixed-valence metal ions in solution, offering a new avenue and opportunity for applications in biochemistry, environmental science, catalysis and materials science.

Towards structural optimization of gold nanoclusters with quantum Monte Carlo.

We study the prospects of using quantum Monte Carlo techniques (QMC) to optimize the electronic wavefunctions and atomic geometries of gold compounds. Complex gold nanoclusters are widely studied for diverse biochemical applications, but the dynamic correlation and relativistic effects in gold set the bar high for reliable, predictive simulation methods. Here we study selected ground state properties of few-atom gold clusters by using density functional theory (DFT) and various implementations of the variational Monte Carlo (VMC) and diffusion Monte Carlo. We show that the QMC methods mitigate the exchange-correlation (XC) approximation made in the DFT approach: the average QMC results are more accurate and significantly more consistent than corresponding DFT results based on different XC functionals. Furthermore, we use demonstrate structural optimization of selected thiolated gold clusters with between 1 and 3 gold atoms using VMC forces. The optimization workflow is demonstrably consistent, robust, and its computational cost scales with nb, where b < 3 and n is the system size. We discuss the implications of these results while laying out steps for further developments.

Simultaneous measurement of temperature and refractive index based on plastic optical fiber knots and F–P interferometer

A reflective sensor based on F–P interferometer (FPI) and plastic optical fiber (POF) knots is proposed for simultaneously measuring the temperature and refractive index (RI). The FPI is fabricated by curing a polyvinyl chloride film on the end of a POF, and it is used to detect the temperature shifts. Meanwhile, the high sensitivity measurement of RI of the glucose solution is realized based on the POF knots. Finally, the RI and temperature are detected simultaneously with the help of the wavelength and reflected light intensity of an interference peak. The experimental results indicate that the proposed sensor achieves a maximum RI sensitivity of 2381.73%/RIU in the RI range of 1.33–1.374, and it can detect temperature simultaneously. The maximum relative deviations between the measured results and actual values of RI and temperature are only 0.038% and 2.76% respectively, and they have good repeatability. Furthermore, the proposed sensor has potential applications in biochemistry and food safety monitoring due to the unmodified and simple preparation process.

Semi- Analytical Study on Non-Isothermal Steady R-D Equation in a Spherical Catalyst and Biocatalyst

The Lane-Emden Boundary Value Problem as it appears in chemical applications, science, and biochemical applications are employed. Two specific models are solved by applying the Ananthaswamy-Sivasankari method (ASM). The model in first problem is a reaction–diffusion equation of a spherical catalyst and the model in second problem is the reaction–diffusion process of a spherical biocatalyst. Obtain a reliable semi-analytical expression of the effectiveness factors and the concentrations. A graph is constructed for the obtained semi-analytical solutions.The effects of several parameters like dimensionless activation energy, Thiele modulus and dimensionless heat of reaction are shown in graphical representation. Our semi-analytical solution is compared with numerical simulation by using MATLAB and finds good fit in all parameters. The new analytical method ASM is helpful to solve many non-linear problems mainly Reaction-Diffusion equation.

Reactivity Umpolung of Amides in Organic Synthesis

AbstractAmides are important carboxylic acid derivatives, having wide applications in chemistry, biochemistry, and material science. Due to the conjugation (nN‐π*C=O), the carbonyl group of amides is the least electrophilic and the Calpha−H bond of amides is the least acidic among the carbonyl derivatives, thereby making it challenging to develop highly efficient and selective transformations based on amides. Reactivity umpolung refers to the reversion of polarity of a functional group. The idea of inverting the innate polarity of organic functional groups, initially introduced by Wittig and later popularized by Seebach, marks a pivotal conceptual breakthrough in organic synthesis. In contrast to the progress for the umpolung of aldehyde, the umpolung of amides has proved challenging and only recently made notable progress. Following the elegant design, the C1 of the amide can become nucleophilic, and the C2 can be electrophilic. In this review, we attempt to summarize the reported examples that are broadly categorized as reactivity umpolung of amides. This review is structured around the umpolung of C1 through radical or carbanion reactions, as well as the umpolung of C2 through electrophilic amide activation or the unique properties of Weinreb amide.

Optimization strategy for inulinase production by Aspergillus niger URM5741 and its biochemical characterization, kinetic/thermodynamic study, and application on inulin and sucrose hydrolysis.

Inulinases are enzymes of great interest in the food industry, especially due to their application in the synthesis of fructose and fructo-oligosaccharides. Moreover, some inulinases (I) also present invertase activity (S), making them useful for sucrose hydrolysis processes. In the present study, the production of inulinase by Aspergillus niger URM5741 was evaluated and optimized using two statistical approaches. First, the composition of the cultivation medium was determined through a simplex centroid mixture design, followed by the selection of optimal fermentation conditions using the Box-Behnken design. Based on these experimental designs, the maximum activities of inulinase (16.68 U mL-1) and invertase (27.80 U mL-1) were achieved using a mixture of wheat, soy, and oat brans (5g), along with 2.5% inulin and 40% moisture. The inulinase exhibited optimum temperature and pH of 60°C and 4.0, respectively, displayed a high affinity for both substrates, as evidenced by very-low Michaelis constant values (1.07-1.54mM). A relative thermostability was observed at 55-60°C as indicated by half-lives values (I: 169.06-137.27min; S: 173.29-141.52min) and D-values (I: 561.61-456.00min; S: 575.65-470.11min) which were further confirmed by the high activation energy (123.01 and 143.29kJmol-1). The enzyme demonstrated favorable results in terms of inulin and sucrose hydrolysis, being a maximum release of reducing sugars of 6.04 and 15.80g L-1, respectively. These results indicate that the sequential statistical approach proved to be beneficial to produce inulinase by A. niger URM5741, with the obtained enzyme considered promising for long-term industrial applications.

A cascade splicing-based multimode fiber-tapered single-mode fiber structure for pressure sensing

Pressure sensing holds immense significance in the realm of fiber optic sensors, particularly in the context of industrial and environmental safety monitoring. In this paper, we propose and experimentally validate an optical fiber structural sensor based on Mach-Zehnder interferometer (MZI) for pressure measurement. The sensor adopts a cascaded spliced single-mode-multimode-tapered single-mode fiber (SMF-MMFTapered SMF, SMTS) structure, taking advantage of the mode mismatch effect between different fiber types and the high sensitivity of the evanescent field surrounding the tapered single-mode fiber. A segment of multimode fiber (MMF) is incorporated as the mode coupler to enhance the multimode interference (MMI). Experimental results demonstrated the sensor's robustness to pressure and temperature changes, with measurement sensitivities of the interference wavelengths Dip A and Dip B at 5.751 nm/KPa and 1.394 nm/KPa, respectively, within the pressure range of 0 ∼ 4410 Pa. The sensor also exhibited a response of 1.113 nm/°C and 0.857 nm/°C in the temperature range of 27.5 °C ∼ 41 °C. The sensor indicates a low temperature crosstalk of only 0.194 KPa/°C. By applying temperature compensation to correct pressure measurements, the accuracy of pressure sensing can be significantly improved. The sensor offers distinct advantages, including high sensitivity, low temperature crosstalk, compact structure, and simple fabrication, making it a promising candidate for applications in biochemistry and industrial production.

Multi-target Fluid Mixing in MEDA Biochips: Theory and an Attempt toward Waste Minimization

Sample preparation is an inherent procedure of many biochemical applications, and digital microfluidic biochips (DMBs) have proved to be very effective in performing such a procedure. In a single mixing step, conventional DMBs can mix two droplets in a 1:1 ratio only. Due to this limitation, DMBs suffer from heavy fluid wastage and often require a lot of mixing steps. However, the next-generation DMBs, i.e., micro-electrode-dot-array (MEDA) biochips, can realize multiple mixing ratios, which in general helps in minimizing the number of mixing operations. In this article, we present a heuristic-based sample preparation algorithm, specifically a mixing algorithm calledDivision by Factor Method for MEDAthat exploits the mixing models of MEDA biochips. We propose another mixing algorithm for MEDA biochips calledSingle Target Waste Minimization(STWM), which minimizes the wastage of fluids and determines an efficient mixing graph. We also propose an advanced methodology for multiple target reagent mixing problems calledMulti-target Waste Minimization(MTWM), which determines efficient mixing graphs for different target ratios by maximizing the sharing of fluids and minimizing the fluid wastage. Simulation results suggest that the proposedSTWMandMTWMmethods outperform the state-of-the-art methods in terms of minimizing the amount of fluid wastage, reducing the total usage of reagent fluids, and minimizing the number of mixing operations.

Stationary concentration of 1O2 over 1O2 quantum yield: Next level of photoactivity analysis

The investigation of the activity of photosensitizers is a multivariate challenge for their further application in photocatalysis. Porphyrins are attractive photoactive molecules for chemical and biochemical applications, while their observed photocatalytic efficiency is a function of a variety of characteristics. In the present work the influence of porphyrin substituents on their photoactivity and photostability along with the solvent effect were studied and discussed in details. Series of experiments with 9,10-diphenylanthracene (DPA) as a selective 1O2 trap allowed to develop the approach for direct measurement of [1O2] and quantitatively evaluate the influence of various factors onto it. The processes of 1O2 relaxation, as well as its chemical and physical quenching were separated and analyzed individually. A kinetic scheme for the photosensitization process was treated with steady-state approximation to develop a mathematical apparatus, where a non-linear dependence between photosensitizer and singlet oxygen concentration was found. The general character of the derived non-linear dependence was proved experimentally for each studied porphyrin. Physical and chemical quenching rate constants of the studied porphyrins were calculated. DFT calculations allowed to find an empirical correlation between HOMO energies and observed rate constants. A plausible reaction mechanism between TPP and 1O2 was examined with Fast-NEB-TS method.

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation

BackgroundThe gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples.ResultsThe pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes.ConclusionsOur study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife.6KUVWwvzFXHebBwiyZoAvnVideo

Biological Application of the Allopathic Characteristics of the Genus Maclura: A Review.

Maclura is a plant genus little known and used, species of which have been mainly used in the recovery of soils, for medicinal purposes such as dental infection treatments, and as wood for making furniture and construction. The overexploitation of this genus has placed certain species in endangered extinction status in some countries, such as Brazil. In addition, the scarce research and information limit the development, cultivation, and management of its species regarding their biochemical composition, which includes bioactive compounds such as the phenolic and flavonoid compounds found in some species such as M. pomifera, M. cochinchinensis, and M. tinctoria. The plants' antioxidant, antimicrobial, anticancer, anti-inflammatory, and antiproliferative activities have been attributed to these compounds. Other biochemical components such as ashes, insoluble lignin, holocellulose, and the high content of lipids and carbohydrates have been identified to be used to produce biofuels, with characteristics very similar to fuels derived from petroleum. This review aims to analyze the current knowledge on the plant genus Maclura, exploring its biochemical compounds and potential applications, including as a food additive, antioxidant supplement, in agriculture, for therapeutic purposes, aquaculture, and the cosmetic and industrial sector.

Agarose fibers with glycerol and graphene oxide and functional properties for potential application in biomaterials

Agarose has numerous applications in biochemistry and medical textiles. This study aimed to produce agarose-graphene oxide-glycerol fibers and analyze their properties. The agarose gel was prepared by dissolving the polymer in 9:1 (v/v) dimethyl sulfoxide (DMSO): H2O, followed by spinning in an ethanol bath (1:1 (v/v) ethanol: H2O) at 20 °C. Fibers were obtained using 8 % (m/v) agarose, 2 % (m/v) glycerol, and 0.5 % and 1 % (m/v) graphene oxide (GO). The fibers had a titer of 18.32–32.49 tex and, a tenacity of 1.40–3.35 cN/tex. GO increased the thermal resistance by 79 %. The presence of glycerol and GO was confirmed and analyzed by FTIR and XPS. Fiber water absorption was decreased by 30 % with the GO addition. The weight loss increased by 55 % after glycerol addition, 51 % with GO addition, and 36 % with glycerol and GO simultaneous addition. Furthermore, GO exhibited 100 % inhibition for both S. aureus (gram-positive) and E. coli bacteria (gram-negative). Fiber F1, with only agarose, inhibited S. aureus by 34.93 %, F2 with 2 % glycerol by 48.72 %, F3 with 0.5 % GO by 63.42 %, and F4 with 2 % glycerol and 0.5 % GO by 30.65 %. However, the inhibition increased to 49.43 % with 1 % GO. The agarose fibers showed low inhibition for E. coli, ranging from 3.35 to 12.12 %.

High-resolution biosensing with C-band guided-mode Fano resonance in an all-dielectric structure

An all-dielectric Fano resonance sensor is proposed, and its sensing characteristics are numerically investigated in the near-infrared region. The proposed device comprises two planar waveguides and a grating. The coupling between high- and low-quality-factor guided modes of the waveguides leads to a sharp Fano resonance at the optical communication wavelength of . Owing to the transparency of constituent dielectric layers in the near-infrared region, a sharp, low-loss Fano resonance appears in the reflection spectrum, which is favorable in sensing applications. The proposed sensor can detect small changes in the refractive index of the sensing medium as low as . The high sensitivity of a structure is promising in biochemical applications, such as measuring the refractive indices of organic solvents, the level of water content in ethanol and aqueous solutions, and blood glucose levels. The refractive index sensitivity is as high as λ=1550nm, and a figure of merit of Δn=0.001 is achieved.